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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 3-46922265-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=46922265&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 46922265,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_144716.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.389G>C",
"hgvs_p": "p.Arg130Pro",
"transcript": "NM_001277074.2",
"protein_id": "NP_001264003.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 166,
"cds_start": 389,
"cds_end": null,
"cds_length": 501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000683445.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001277074.2"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.389G>C",
"hgvs_p": "p.Arg130Pro",
"transcript": "ENST00000683445.1",
"protein_id": "ENSP00000508011.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 166,
"cds_start": 389,
"cds_end": null,
"cds_length": 501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001277074.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000683445.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.515G>C",
"hgvs_p": "p.Arg172Pro",
"transcript": "ENST00000878135.1",
"protein_id": "ENSP00000548194.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 208,
"cds_start": 515,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878135.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.491G>C",
"hgvs_p": "p.Arg164Pro",
"transcript": "ENST00000878137.1",
"protein_id": "ENSP00000548196.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 200,
"cds_start": 491,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878137.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.389G>C",
"hgvs_p": "p.Arg130Pro",
"transcript": "ENST00000718454.1",
"protein_id": "ENSP00000520832.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 197,
"cds_start": 389,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000718454.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.428G>C",
"hgvs_p": "p.Arg143Pro",
"transcript": "NM_144716.6",
"protein_id": "NP_653317.2",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 179,
"cds_start": 428,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_144716.6"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.428G>C",
"hgvs_p": "p.Arg143Pro",
"transcript": "ENST00000292314.6",
"protein_id": "ENSP00000292314.2",
"transcript_support_level": 5,
"aa_start": 143,
"aa_end": null,
"aa_length": 179,
"cds_start": 428,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000292314.6"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.389G>C",
"hgvs_p": "p.Arg130Pro",
"transcript": "ENST00000425441.5",
"protein_id": "ENSP00000416263.2",
"transcript_support_level": 5,
"aa_start": 130,
"aa_end": null,
"aa_length": 166,
"cds_start": 389,
"cds_end": null,
"cds_length": 501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000425441.5"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.383G>C",
"hgvs_p": "p.Arg128Pro",
"transcript": "ENST00000928986.1",
"protein_id": "ENSP00000599045.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 164,
"cds_start": 383,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928986.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "c.380G>C",
"hgvs_p": "p.Arg127Pro",
"transcript": "ENST00000878136.1",
"protein_id": "ENSP00000548195.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 163,
"cds_start": 380,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878136.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "n.1895G>C",
"hgvs_p": null,
"transcript": "ENST00000604367.1",
"protein_id": null,
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000604367.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "n.442G>C",
"hgvs_p": null,
"transcript": "NR_102269.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_102269.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"hgvs_c": "n.*40G>C",
"hgvs_p": null,
"transcript": "ENST00000605358.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000605358.5"
}
],
"gene_symbol": "CCDC12",
"gene_hgnc_id": 28332,
"dbsnp": "rs146091475",
"frequency_reference_population": 6.840441e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84044e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.839081883430481,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.665,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9795,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.44,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.408,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_144716.6",
"gene_symbol": "CCDC12",
"hgnc_id": 28332,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.428G>C",
"hgvs_p": "p.Arg143Pro"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}